Single cell type - USP8 - The Human Protein Atlas

USP8

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Pathway

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.	USP8
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 8
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Enzymes Human disease related genes Metabolic proteins Potential drug targets
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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.	Non-specific - Transcription (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.	Low cell type specificity
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.25
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	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.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Low cell type specificity

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

USP8 is part of cluster 55 Non-specific - Transcription with confidenceⁱ 1
709 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
RNMT	RNA guanine-7 methyltransferase	0.5723	78
PHF3	PHD finger protein 3	0.5340	55
SCAF11	SR-related CTD associated factor 11	0.5262	55
ANKRD11	Ankyrin repeat domain containing 11	0.5245	28
SLU7	SLU7 homolog, splicing factor	0.5245	55
BCLAF1	BCL2 associated transcription factor 1	0.5162	78
BDP1	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	0.5156	55
PRPF40A	Pre-mRNA processing factor 40 homolog A	0.5089	39
DHX38	DEAH-box helicase 38	0.4891	55
USP7	Ubiquitin specific peptidase 7	0.4890	18
RBM25	RNA binding motif protein 25	0.4844	55
PRPF4B	Pre-mRNA processing factor 4B	0.4812	78
GGNBP2	Gametogenetin binding protein 2	0.4706	70
DIS3	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	0.4649	55
AKAP8	A-kinase anchoring protein 8	0.4646	80

IMMUNE CELLS

USP8 is part of cluster 32 Basophils - Transcription with confidenceⁱ 0.63
291 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
FAM86B1	Family with sequence similarity 86 member B1	1.0000	32
RAB31	RAB31, member RAS oncogene family	1.0000	32
TP53INP1	Tumor protein p53 inducible nuclear protein 1	1.0000	32
ZFPL1	Zinc finger protein like 1	1.0000	32
INO80C	INO80 complex subunit C	1.0000	32
SPDYE1	Speedy/RINGO cell cycle regulator family member E1	1.0000	32
JAK2	Janus kinase 2	0.9762	46
KDM5B	Lysine demethylase 5B	0.9762	46
VAT1	Vesicle amine transport 1	0.9762	32
FAH	Fumarylacetoacetate hydrolase	0.9762	46
BTK	Bruton tyrosine kinase	0.9762	32
ZFAND6	Zinc finger AN1-type containing 6	0.9762	32
EFR3B	EFR3 homolog B	0.9762	32
DHRS9	Dehydrogenase/reductase 9	0.9762	46
TMEM38A	Transmembrane protein 38A	0.9762	32

Adipocytes	61.7 nTPM
Adipose tissue	64.1 nTPM
Breast	59.3 nTPM

Alveolar cells type 1	53.0 nTPM
Lung	53.0 nTPM

Alveolar cells type 2	74.7 nTPM
Lung	74.7 nTPM

Astrocytes	34.4 nTPM
Brain	34.4 nTPM

B-cells	90.6 nTPM
Adipose tissue	183.9 nTPM
Salivary gland	169.5 nTPM
PBMC	135.5 nTPM
Stomach	124.4 nTPM
Lymph node	117.1 nTPM
Thymus	88.7 nTPM
Spleen	82.0 nTPM
Lung	64.4 nTPM
Bone marrow	57.1 nTPM
Liver	48.3 nTPM
Kidney	46.8 nTPM
Skin	30.5 nTPM
Esophagus	29.5 nTPM

Ciliated cells	75.4 nTPM
Endometrium	87.2 nTPM
Lung	77.3 nTPM
Bronchus	69.1 nTPM
Fallopian tube	67.9 nTPM

Club cells	53.3 nTPM
Prostate	62.1 nTPM
Bronchus	52.0 nTPM
Lung	45.6 nTPM

Dendritic cells	115.5 nTPM
Adipose tissue	166.3 nTPM
PBMC	64.8 nTPM

Endothelial cells	57.7 nTPM
Heart muscle	97.6 nTPM
Skeletal muscle	81.7 nTPM
Salivary gland	80.0 nTPM
Vascular	67.8 nTPM
Thymus	60.8 nTPM
Liver	59.2 nTPM
Testis	58.6 nTPM
Prostate	56.2 nTPM
Endometrium	56.0 nTPM
Fallopian tube	55.6 nTPM
Ovary	54.5 nTPM
Pancreas	54.3 nTPM
Breast	50.1 nTPM
Lung	47.9 nTPM
Tongue	45.0 nTPM
Placenta	43.7 nTPM
Skin	35.3 nTPM
Esophagus	34.1 nTPM

Enteroendocrine cells	55.9 nTPM
Small intestine	61.8 nTPM
Colon	60.5 nTPM
Rectum	45.3 nTPM

Fibroblasts	55.9 nTPM
Salivary gland	88.8 nTPM
Skeletal muscle	79.2 nTPM
Liver	68.8 nTPM
Fallopian tube	65.9 nTPM
Vascular	65.5 nTPM
Heart muscle	62.0 nTPM
Breast	60.9 nTPM
Adipose tissue	60.4 nTPM
Prostate	54.8 nTPM
Thymus	54.3 nTPM
Pancreas	47.4 nTPM
Esophagus	42.9 nTPM
Skin	42.8 nTPM
Lung	39.7 nTPM
Placenta	30.5 nTPM
Stomach	30.3 nTPM

Granulocytes	51.6 nTPM
Fallopian tube	60.7 nTPM
Lung	50.4 nTPM
Tongue	43.7 nTPM

Intestinal goblet cells	59.5 nTPM
Small intestine	70.1 nTPM
Colon	60.3 nTPM
Rectum	48.1 nTPM

Lymphatic endothelial cells	55.5 nTPM
Fallopian tube	62.0 nTPM
Ovary	49.1 nTPM

Macrophages	77.7 nTPM
Skeletal muscle	122.5 nTPM
Adipose tissue	114.8 nTPM
Fallopian tube	103.1 nTPM
Vascular	101.7 nTPM
Salivary gland	89.6 nTPM
Bone marrow	89.2 nTPM
Lung	86.3 nTPM
Thymus	86.1 nTPM
Spleen	79.2 nTPM
Breast	74.6 nTPM
Tongue	73.2 nTPM
Endometrium	69.5 nTPM
Prostate	62.9 nTPM
Pancreas	61.7 nTPM
Stomach	61.7 nTPM
Esophagus	59.1 nTPM
Testis	55.8 nTPM
Kidney	42.5 nTPM
Skin	42.3 nTPM

Basal keratinocytes	44.3 nTPM
Tongue	49.5 nTPM
Skin	39.0 nTPM

Basal prostatic cells	53.4 nTPM
Prostate	53.4 nTPM

Basal squamous epithelial cells	37.0 nTPM
Esophagus	37.0 nTPM

Bipolar cells	47.6 nTPM
Eye	47.6 nTPM

Paneth cells	61.6 nTPM
Colon	72.4 nTPM
Rectum	57.1 nTPM
Small intestine	55.3 nTPM

Plasma cells	71.9 nTPM
Fallopian tube	96.8 nTPM
Salivary gland	90.9 nTPM
Spleen	88.5 nTPM
Stomach	84.6 nTPM
Thymus	59.4 nTPM
Liver	55.6 nTPM
Bone marrow	52.9 nTPM
Esophagus	46.8 nTPM

Schwann cells	67.7 nTPM
Adipose tissue	103.5 nTPM
Vascular	75.7 nTPM
Esophagus	24.0 nTPM

Serous glandular cells	61.7 nTPM
Salivary gland	74.8 nTPM
Tongue	48.6 nTPM

Smooth muscle cells	54.8 nTPM
Skeletal muscle	87.7 nTPM
Vascular	71.5 nTPM
Salivary gland	63.4 nTPM
Endometrium	62.3 nTPM
Tongue	62.0 nTPM
Adipose tissue	61.2 nTPM
Prostate	52.9 nTPM
Fallopian tube	51.7 nTPM
Ovary	51.4 nTPM
Liver	49.7 nTPM
Thymus	48.3 nTPM
Lung	48.2 nTPM
Placenta	47.1 nTPM
Breast	46.3 nTPM
Skin	38.2 nTPM
Esophagus	34.8 nTPM

Suprabasal keratinocytes	53.4 nTPM
Tongue	61.4 nTPM
Skin	45.5 nTPM

T-cells	70.4 nTPM
Adipose tissue	129.9 nTPM
Skeletal muscle	106.6 nTPM
Salivary gland	97.2 nTPM
Fallopian tube	91.7 nTPM
PBMC	84.0 nTPM
Breast	82.6 nTPM
Tongue	79.2 nTPM
Vascular	74.4 nTPM
Endometrium	69.7 nTPM
Colon	66.3 nTPM
Lung	63.6 nTPM
Prostate	61.8 nTPM
Lymph node	59.0 nTPM
Stomach	57.7 nTPM
Thymus	57.1 nTPM
Spleen	56.5 nTPM
Esophagus	53.5 nTPM
Liver	51.1 nTPM
Skin	48.4 nTPM
Kidney	45.2 nTPM
Bone marrow	42.6 nTPM

Undifferentiated cells	55.1 nTPM
Small intestine	63.4 nTPM
Rectum	53.9 nTPM
Colon	48.0 nTPM

Amygdala excitatory	76.6 nTPM
Hypothalamus	89.4 nTPM
Amygdala	85.7 nTPM
Hippocampus	79.7 nTPM
Cerebral cortex	76.6 nTPM
Basal ganglia	71.7 nTPM
Thalamus	56.7 nTPM

Astrocyte	74.8 nTPM
Amygdala	93.7 nTPM
Thalamus	84.5 nTPM
Hypothalamus	80.2 nTPM
Cerebellum	77.9 nTPM
Cerebral cortex	76.0 nTPM
Midbrain	76.0 nTPM
Basal ganglia	74.5 nTPM
Hippocampus	74.5 nTPM
Pons	69.9 nTPM
Medulla oblongata	61.4 nTPM
Spinal cord	53.9 nTPM

Bergmann glia	75.4 nTPM
Medulla oblongata	83.1 nTPM
Cerebellum	79.8 nTPM
Pons	63.3 nTPM

Central nervous system macrophage	123.1 nTPM
Amygdala	166.7 nTPM
Thalamus	128.1 nTPM
Hypothalamus	126.7 nTPM
Midbrain	125.6 nTPM
Hippocampus	124.9 nTPM
Basal ganglia	120.8 nTPM
Cerebral cortex	120.2 nTPM
Cerebellum	118.1 nTPM
Pons	117.6 nTPM
Spinal cord	107.2 nTPM
Medulla oblongata	98.0 nTPM

Cerebellar inhibitory	88.7 nTPM
Midbrain	101.1 nTPM
Medulla oblongata	88.4 nTPM
Cerebellum	86.1 nTPM
Spinal cord	85.2 nTPM
Pons	82.8 nTPM

Cge interneuron	65.5 nTPM
Hypothalamus	74.8 nTPM
Midbrain	68.0 nTPM
Amygdala	67.5 nTPM
Thalamus	66.2 nTPM
Hippocampus	60.9 nTPM
Cerebral cortex	60.6 nTPM
Basal ganglia	60.2 nTPM

Choroid plexus epithelial cell	110.9 nTPM
Basal ganglia	161.2 nTPM
Medulla oblongata	108.7 nTPM
Hippocampus	88.7 nTPM
Thalamus	85.0 nTPM

Committed oligodendrocyte precursor	73.7 nTPM
Thalamus	91.6 nTPM
Hypothalamus	89.4 nTPM
Spinal cord	84.6 nTPM
Hippocampus	80.5 nTPM
Amygdala	78.9 nTPM
Midbrain	77.3 nTPM
Cerebral cortex	67.8 nTPM
Medulla oblongata	67.1 nTPM
Basal ganglia	60.8 nTPM
Cerebellum	57.1 nTPM
Pons	55.8 nTPM

Deep-layer corticothalamic and 6b	63.5 nTPM
Hypothalamus	74.1 nTPM
Cerebral cortex	65.4 nTPM
Amygdala	64.5 nTPM
Hippocampus	63.6 nTPM
Basal ganglia	56.8 nTPM
Midbrain	56.6 nTPM

Deep-layer intratelencephalic	70.3 nTPM
Hypothalamus	83.8 nTPM
Hippocampus	70.8 nTPM
Amygdala	69.4 nTPM
Cerebral cortex	65.6 nTPM
Basal ganglia	61.8 nTPM

Deep-layer near-projecting	62.9 nTPM
Hypothalamus	76.6 nTPM
Cerebral cortex	63.9 nTPM
Amygdala	62.3 nTPM
Basal ganglia	56.6 nTPM
Hippocampus	55.3 nTPM

Eccentric medium spiny neuron	68.0 nTPM
Hippocampus	77.5 nTPM
Amygdala	72.4 nTPM
Thalamus	67.3 nTPM
Cerebral cortex	64.4 nTPM
Hypothalamus	64.4 nTPM
Basal ganglia	62.3 nTPM