Single cell type - USP3 - The Human Protein Atlas

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.	USP3
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic 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.	9

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Monocytes & Neutrophils - Innate immune response (mainly)
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	Low cell type specificity
Immune 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 immune cell specificity
Immune 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. Read more	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. Read more	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 (nTPM) 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: Low cell type specificity

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

USP3 is part of cluster 19 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 1
175 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
MTMR3	Myotubularin related protein 3	0.5335	64
GPCPD1	Glycerophosphocholine phosphodiesterase 1	0.5181	19
BRWD3	Bromodomain and WD repeat domain containing 3	0.5025	44
MBD2	Methyl-CpG binding domain protein 2	0.5011	41
BACH1	BTB domain and CNC homolog 1	0.4930	41
CD300E	CD300e molecule	0.4925	19
NOD2	Nucleotide binding oligomerization domain containing 2	0.4916	19
RIPK2	Receptor interacting serine/threonine kinase 2	0.4915	41
HIF1A	Hypoxia inducible factor 1 subunit alpha	0.4881	40
ADGRE1	Adhesion G protein-coupled receptor E1	0.4824	19
FPR2	Formyl peptide receptor 2	0.4812	41
CREBBP	CREB binding protein	0.4798	44
PLAGL2	PLAG1 like zinc finger 2	0.4795	31
FPR1	Formyl peptide receptor 1	0.4769	19
S100Z	S100 calcium binding protein Z	0.4740	19

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated 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 Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	23.6 nTPM
Breast	26.3 nTPM
Adipose tissue	21.0 nTPM

Alveolar cells type 1	38.5 nTPM
Lung	38.5 nTPM

Alveolar cells type 2	69.2 nTPM
Lung	69.2 nTPM

Astrocytes	76.7 nTPM
Brain	76.7 nTPM

B-cells	63.4 nTPM
Adipose tissue	104.3 nTPM
Lymph node	80.7 nTPM
Stomach	74.5 nTPM
Colon	67.1 nTPM
Breast	64.1 nTPM
PBMC	60.0 nTPM
Spleen	58.2 nTPM
Bone marrow	52.3 nTPM
Liver	39.1 nTPM
Kidney	33.4 nTPM

Dendritic cells	48.4 nTPM
Adipose tissue	81.0 nTPM
Breast	52.1 nTPM
PBMC	12.0 nTPM

Endothelial cells	26.0 nTPM
Prostate	48.4 nTPM
Skin	40.7 nTPM
Endometrium	36.7 nTPM
Lung	28.1 nTPM
Esophagus	27.3 nTPM
Pancreas	27.0 nTPM
Ovary	25.5 nTPM
Breast	25.1 nTPM
Eye	21.8 nTPM
Testis	20.1 nTPM
Skeletal muscle	19.4 nTPM
Placenta	18.8 nTPM
Liver	14.7 nTPM
Heart muscle	9.8 nTPM

Fibroblasts	28.3 nTPM
Lung	54.7 nTPM
Prostate	40.4 nTPM
Skin	38.4 nTPM
Stomach	28.2 nTPM
Adipose tissue	27.0 nTPM
Ovary	25.6 nTPM
Skeletal muscle	25.4 nTPM
Breast	24.0 nTPM
Esophagus	23.4 nTPM
Heart muscle	15.0 nTPM
Placenta	8.7 nTPM

Intestinal goblet cells	35.4 nTPM
Rectum	38.0 nTPM
Colon	37.1 nTPM
Small intestine	31.2 nTPM

Macrophages	74.5 nTPM
Stomach	149.5 nTPM
Adipose tissue	139.9 nTPM
Skeletal muscle	99.8 nTPM
Lung	98.5 nTPM
Spleen	92.3 nTPM
Bone marrow	87.5 nTPM
Esophagus	77.1 nTPM
Testis	70.9 nTPM
Endometrium	63.6 nTPM
Ovary	60.9 nTPM
Kidney	60.5 nTPM
Breast	48.4 nTPM
Prostate	40.1 nTPM
Pancreas	15.3 nTPM
PBMC	13.6 nTPM

Paneth cells	35.6 nTPM
Rectum	44.3 nTPM
Colon	36.2 nTPM
Small intestine	26.3 nTPM

Plasma cells	69.7 nTPM
Adipose tissue	110.2 nTPM
Spleen	71.5 nTPM
Stomach	65.2 nTPM
Esophagus	55.5 nTPM
Bone marrow	46.2 nTPM

Respiratory ciliated cells	33.3 nTPM
Lung	39.4 nTPM
Bronchus	27.1 nTPM

Smooth muscle cells	34.5 nTPM
Bronchus	71.0 nTPM
Ovary	46.9 nTPM
Prostate	41.8 nTPM
Endometrium	35.6 nTPM
Skin	35.2 nTPM
Esophagus	31.0 nTPM
Heart muscle	27.8 nTPM
Adipose tissue	27.0 nTPM
Pancreas	22.4 nTPM
Breast	22.4 nTPM
Skeletal muscle	18.3 nTPM

T-cells	64.6 nTPM
Adipose tissue	130.6 nTPM
Lung	112.4 nTPM
Lymph node	94.4 nTPM
Skeletal muscle	86.1 nTPM
Skin	82.0 nTPM
Spleen	70.0 nTPM
Endometrium	66.6 nTPM
Breast	62.7 nTPM
PBMC	53.5 nTPM
Stomach	51.7 nTPM
Bone marrow	51.5 nTPM
Colon	49.4 nTPM
Kidney	46.5 nTPM
Prostate	37.9 nTPM
Ovary	35.6 nTPM
Liver	35.3 nTPM
Esophagus	32.8 nTPM

Basal keratinocytes	52.6 nTPM
Skin	52.6 nTPM

Basal prostatic cells	34.3 nTPM
Prostate	34.3 nTPM

Basal respiratory cells	24.8 nTPM
Bronchus	24.8 nTPM

Basal squamous epithelial cells	23.3 nTPM
Esophagus	23.3 nTPM

Undifferentiated cells	40.6 nTPM
Colon	43.9 nTPM
Rectum	43.9 nTPM
Small intestine	34.0 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC