Cell type atlas - VAT1 - The Human Protein Atlas

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VAT1

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.	VAT1
Gene descriptionⁱ Full gene name according to HGNC.	Vesicle amine transport 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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	Cell type enhanced (Hofbauer cells, Melanocytes)
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 all
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 (SK-MEL-30)
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 all
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: Cell type enhanced (Hofbauer cells, Melanocytes)

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	21 NX
Lung	21 NX

Alveolar cells type 2	15 NX
Lung	15 NX

B-cells	13 NX
Kidney	13 NX
Colon	12 NX
Liver	8 NX

Basal glandular cells	13 NX
Prostate	13 NX

Basal keratinocytes	25 NX
Skin	25 NX

Bipolar cells	1 NX
Eye	1 NX

Cardiomyocytes	29 NX
Heart muscle	29 NX

Cholangiocytes	26 NX
Liver	26 NX

Ciliated cells	8 NX
Lung	8 NX

Club cells	3 NX
Lung	3 NX

Collecting duct cells	23 NX
Kidney	23 NX

Cone photoreceptor cells	4 NX
Eye	4 NX

Cytotrophoblasts	5 NX
Placenta	5 NX

Distal tubular cells	15 NX
Kidney	15 NX

Ductal cells	86 NX
Pancreas	86 NX

Early spermatids	19 NX
Testis	19 NX

Endothelial cells	60 NX
Liver	126 NX
Placenta	87 NX
Pancreas	82 NX
Testis	68 NX
Skin	61 NX
Prostate	50 NX
Heart muscle	47 NX
Lung	26 NX
Eye	21 NX

Enterocytes	10 NX
Small intestine	31 NX
Rectum	8 NX
Colon	7 NX

Erythroid cells	0 NX
Liver	0 NX

Exocrine glandular cells	38 NX
Pancreas	38 NX

Extravillous trophoblasts	40 NX
Placenta	40 NX

Fibroblasts	34 NX
Skin	73 NX
Heart muscle	56 NX
Prostate	30 NX
Placenta	26 NX
Lung	22 NX

Glandular cells	19 NX
Prostate	19 NX

Granulocytes	74 NX
Lung	93 NX
Colon	55 NX

Hepatocytes	14 NX
Liver	14 NX

Hofbauer cells	127 NX
Placenta	127 NX

Horizontal cells	5 NX
Eye	5 NX

Intestinal endocrine cells	15 NX
Rectum	26 NX
Colon	3 NX

Ito cells	72 NX
Liver	72 NX

Kupffer cells	37 NX
Liver	37 NX

Late spermatids	32 NX
Testis	32 NX

Leydig cells	48 NX
Testis	48 NX

Macrophages	27 NX
Pancreas	84 NX
Lung	60 NX
Skin	28 NX
Kidney	27 NX
Prostate	21 NX
Testis	20 NX

Melanocytes	116 NX
Skin	116 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	20 NX
Pancreas	20 NX

Mucus-secreting cells	3 NX
Small intestine	8 NX
Rectum	2 NX
Colon	1 NX

Muller glia cells	3 NX
Eye	3 NX

Pancreatic endocrine cells	60 NX
Pancreas	60 NX

Paneth cells	6 NX
Small intestine	18 NX
Colon	6 NX
Rectum	5 NX

Peritubular cells	55 NX
Testis	55 NX

Proximal tubular cells	39 NX
Kidney	39 NX

Rod photoreceptor cells	2 NX
Eye	2 NX

Sertoli cells	13 NX
Testis	13 NX

Smooth muscle cells	29 NX
Pancreas	97 NX
Skin	34 NX
Heart muscle	19 NX
Prostate	14 NX

Spermatocytes	14 NX
Testis	14 NX

Spermatogonia	7 NX
Testis	7 NX

Suprabasal keratinocytes	29 NX
Skin	29 NX

Syncytiotrophoblasts	9 NX
Placenta	9 NX

T-cells	8 NX
Skin	25 NX
Prostate	13 NX
Kidney	11 NX
Lung	10 NX
Colon	8 NX
Liver	6 NX

Undifferentiated cells	3 NX
Small intestine	5 NX
Rectum	3 NX
Colon	2 NX

Urothelial cells	21 NX
Prostate	21 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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