Cell type atlas - CLGN - The Human Protein Atlas

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CLGN

SUMMARY

TISSUE

CELL TYPE

PATHOLOGY

BRAIN

BLOOD

CELL

GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	CLGN
Gene descriptionⁱ Full gene name according to HGNC.	Calmegin
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Intracellular,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Group enriched (Spermatocytes, Cardiomyocytes, Muller glia cells, Early spermatids)
Blood cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enhanced (basophil)
Blood cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in some
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines.	Cell line enhanced (hTERT-RPE1, U-251 MG)
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines.	Detected in many
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of single cell RNA (NX) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types Group Expression Alphabetical RNA single cell type specificity: Group enriched (Spermatocytes, Cardiomyocytes, Muller glia cells, Early spermatids)

SINGLE CELL TISSUESⁱ Single cell RNA in cell types from tissue are shown separately for each analyzed tissue. For easier navigation across tissues, use the grey browser on the left side of the window. Barchart shows pTPM levels in each cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ RNA expression data (NX) of tissue culture cell lines.The analyzed cell lines are divided into 16 color-coded groups according to the organ they were obtained from. Detailed information about a specific cell line is revealed by hovering over the corresponding bar in the chart. The chart is clickable and redirects to more Cell Atlas data. Read more
Organ Expression Alphabetical

Alveolar cells type 1	0 NX
Lung	0 NX

Alveolar cells type 2	2 NX
Lung	2 NX

B-cells	0 NX
Liver	1 NX
Kidney	0 NX
Colon	0 NX

Basal glandular cells	1 NX
Prostate	1 NX

Basal keratinocytes	0 NX
Skin	0 NX

Bipolar cells	9 NX
Eye	8 NX

Cardiomyocytes	243 NX
Heart muscle	243 NX

Cholangiocytes	0 NX
Liver	0 NX

Ciliated cells	28 NX
Lung	28 NX

Club cells	5 NX
Lung	5 NX

Collecting duct cells	0 NX
Kidney	0 NX

Cone photoreceptor cells	4 NX
Eye	4 NX

Cytotrophoblasts	0 NX
Placenta	0 NX

Distal tubular cells	0 NX
Kidney	0 NX

Ductal cells	1 NX
Pancreas	1 NX

Early spermatids	78 NX
Testis	78 NX

Endothelial cells	1 NX
Testis	112 NX
Heart muscle	15 NX
Placenta	4 NX
Eye	3 NX
Skin	1 NX
Lung	0 NX
Pancreas	0 NX
Prostate	0 NX
Liver	0 NX

Enterocytes	0 NX
Rectum	1 NX
Colon	0 NX
Small intestine	0 NX

Erythroid cells	23 NX
Liver	23 NX

Exocrine glandular cells	4 NX
Pancreas	4 NX

Extravillous trophoblasts	0 NX
Placenta	0 NX

Fibroblasts	1 NX
Heart muscle	95 NX
Prostate	4 NX
Lung	1 NX
Skin	0 NX
Placenta	0 NX

Glandular cells	35 NX
Prostate	35 NX

Granulocytes	0 NX
Colon	0 NX
Lung	0 NX

Hepatocytes	3 NX
Liver	3 NX

Hofbauer cells	0 NX
Placenta	0 NX

Horizontal cells	24 NX
Eye	24 NX

Intestinal endocrine cells	5 NX
Colon	10 NX
Rectum	0 NX

Ito cells	0 NX
Liver	0 NX

Kupffer cells	0 NX
Liver	0 NX

Late spermatids	43 NX
Testis	43 NX

Leydig cells	5 NX
Testis	5 NX

Macrophages	0 NX
Testis	6 NX
Kidney	1 NX
Skin	0 NX
Lung	0 NX
Prostate	0 NX
Pancreas	0 NX

Melanocytes	2 NX
Skin	2 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	0 NX
Pancreas	0 NX

Mucus-secreting cells	0 NX
Rectum	1 NX
Small intestine	0 NX
Colon	0 NX

Muller glia cells	200 NX
Eye	200 NX

Pancreatic endocrine cells	1 NX
Pancreas	1 NX

Paneth cells	0 NX
Rectum	10 NX
Small intestine	0 NX
Colon	0 NX

Peritubular cells	4 NX
Testis	4 NX

Proximal tubular cells	0 NX
Kidney	0 NX

Rod photoreceptor cells	12 NX
Eye	12 NX

Sertoli cells	0 NX
Testis	0 NX

Smooth muscle cells	0 NX
Heart muscle	14 NX
Prostate	1 NX
Skin	0 NX
Pancreas	0 NX

Spermatocytes	281 NX
Testis	281 NX

Spermatogonia	10 NX
Testis	10 NX

Suprabasal keratinocytes	0 NX
Skin	0 NX

Syncytiotrophoblasts	0 NX
Placenta	0 NX

T-cells	0 NX
Prostate	9 NX
Skin	0 NX
Lung	0 NX
Liver	0 NX
Kidney	0 NX
Colon	0 NX

Undifferentiated cells	0 NX
Rectum	2 NX
Small intestine	0 NX
Colon	0 NX

Urothelial cells	1 NX
Prostate	1 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.