Cell type atlas - USP4 - The Human Protein Atlas

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USP4

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.	USP4
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	5

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 (Early spermatids, Late 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	Low cell type specificity
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.	Low cell line specificity
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 (Early spermatids, Late 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	39 NX
Lung	39 NX

Alveolar cells type 2	21 NX
Lung	21 NX

B-cells	18 NX
Liver	23 NX
Colon	18 NX
Kidney	5 NX

Basal glandular cells	15 NX
Prostate	15 NX

Basal keratinocytes	17 NX
Skin	17 NX

Bipolar cells	17 NX
Eye	17 NX

Cardiomyocytes	15 NX
Heart muscle	15 NX

Cholangiocytes	15 NX
Liver	15 NX

Ciliated cells	34 NX
Lung	34 NX

Club cells	25 NX
Lung	25 NX

Collecting duct cells	19 NX
Kidney	19 NX

Cone photoreceptor cells	20 NX
Eye	20 NX

Cytotrophoblasts	19 NX
Placenta	19 NX

Distal tubular cells	18 NX
Kidney	18 NX

Ductal cells	14 NX
Pancreas	14 NX

Early spermatids	100 NX
Testis	100 NX

Endothelial cells	18 NX
Lung	29 NX
Liver	25 NX
Eye	22 NX
Testis	20 NX
Heart muscle	19 NX
Pancreas	18 NX
Placenta	15 NX
Prostate	15 NX
Skin	13 NX

Enterocytes	12 NX
Rectum	15 NX
Small intestine	12 NX
Colon	9 NX

Erythroid cells	0 NX
Liver	0 NX

Exocrine glandular cells	12 NX
Pancreas	12 NX

Extravillous trophoblasts	12 NX
Placenta	12 NX

Fibroblasts	12 NX
Lung	25 NX
Prostate	13 NX
Placenta	12 NX
Heart muscle	12 NX
Skin	11 NX

Glandular cells	13 NX
Prostate	13 NX

Granulocytes	32 NX
Lung	37 NX
Colon	28 NX

Hepatocytes	12 NX
Liver	12 NX

Hofbauer cells	22 NX
Placenta	22 NX

Horizontal cells	11 NX
Eye	11 NX

Intestinal endocrine cells	10 NX
Colon	14 NX
Rectum	7 NX

Ito cells	16 NX
Liver	16 NX

Kupffer cells	39 NX
Liver	39 NX

Late spermatids	90 NX
Testis	90 NX

Leydig cells	14 NX
Testis	14 NX

Macrophages	25 NX
Testis	41 NX
Lung	40 NX
Kidney	31 NX
Prostate	21 NX
Skin	20 NX
Pancreas	19 NX

Melanocytes	15 NX
Skin	15 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	31 NX
Pancreas	31 NX

Mucus-secreting cells	11 NX
Colon	14 NX
Small intestine	14 NX
Rectum	9 NX

Muller glia cells	12 NX
Eye	12 NX

Pancreatic endocrine cells	15 NX
Pancreas	15 NX

Paneth cells	6 NX
Rectum	11 NX
Colon	6 NX
Small intestine	4 NX

Peritubular cells	18 NX
Testis	18 NX

Proximal tubular cells	11 NX
Kidney	11 NX

Rod photoreceptor cells	22 NX
Eye	22 NX

Sertoli cells	13 NX
Testis	13 NX

Smooth muscle cells	15 NX
Skin	17 NX
Prostate	15 NX
Heart muscle	14 NX
Pancreas	13 NX

Spermatocytes	19 NX
Testis	19 NX

Spermatogonia	14 NX
Testis	14 NX

Suprabasal keratinocytes	16 NX
Skin	16 NX

Syncytiotrophoblasts	20 NX
Placenta	20 NX

T-cells	25 NX
Skin	30 NX
Lung	30 NX
Colon	25 NX
Liver	24 NX
Kidney	17 NX
Prostate	9 NX

Undifferentiated cells	12 NX
Colon	13 NX
Rectum	12 NX
Small intestine	11 NX

Urothelial cells	12 NX
Prostate	12 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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