Single cell type - USP20 - The Human Protein Atlas

USP20

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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.	USP20
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 20
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	Intracellular
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 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.	T-cells - T-cell receptor (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.	0.42
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

USP20 is part of cluster 7 T-cells - T-cell receptor with confidenceⁱ 1
246 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.
TRAV12-3	T cell receptor alpha variable 12-3	0.7948	7
TRBV12-4	T cell receptor beta variable 12-4	0.7944	7
TRAV38-1	T cell receptor alpha variable 38-1	0.7922	7
TRBV28	T cell receptor beta variable 28	0.7843	7
TRAV23DV6	T cell receptor alpha variable 23/delta variable 6	0.7820	7
TRAV1-1	T cell receptor alpha variable 1-1	0.7799	7
TRBV12-3	T cell receptor beta variable 12-3	0.7760	7
TRAV5	T cell receptor alpha variable 5	0.7759	7
TRAV20	T cell receptor alpha variable 20	0.7757	7
TRAV13-1	T cell receptor alpha variable 13-1	0.7704	7
TRBV7-9	T cell receptor beta variable 7-9	0.7695	7
SEPTIN1	Septin 1	0.7680	7
TRBV9	T cell receptor beta variable 9	0.7673	7
TRBV14	T cell receptor beta variable 14	0.7659	7
TRAV19	T cell receptor alpha variable 19	0.7629	7

IMMUNE CELLS

USP20 is part of cluster 3 Non-specific - Nuclear processes with confidenceⁱ 0.96
471 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.
ZNF14	Zinc finger protein 14	1.0000	3
PINX1	PIN2 (TERF1) interacting telomerase inhibitor 1	0.9762	3
STMN3	Stathmin 3	0.9762	3
FLT3LG	Fms related receptor tyrosine kinase 3 ligand	0.9762	3
BNIP3	BCL2 interacting protein 3	0.9762	3
RWDD1	RWD domain containing 1	0.9762	3
NAE1	NEDD8 activating enzyme E1 subunit 1	0.9762	3
CCND2	Cyclin D2	0.9762	3
HELB	DNA helicase B	0.9762	3
YEATS4	YEATS domain containing 4	0.9762	3
SMYD2	SET and MYND domain containing 2	0.9762	3
TPRKB	TP53RK binding protein	0.9762	3
BBS2	Bardet-Biedl syndrome 2	0.9524	3
TADA1	Transcriptional adaptor 1	0.9524	3
CACNA2D2	Calcium voltage-gated channel auxiliary subunit alpha2delta 2	0.9524	11

Adipocytes	3.1 nTPM
Breast	3.8 nTPM
Adipose tissue	2.4 nTPM

Alveolar cells type 1	3.0 nTPM
Lung	3.0 nTPM

Alveolar cells type 2	3.8 nTPM
Lung	3.8 nTPM

Astrocytes	15.5 nTPM
Brain	15.5 nTPM

B-cells	7.3 nTPM
Bone marrow	17.9 nTPM
Kidney	15.6 nTPM
Lymph node	11.2 nTPM
Spleen	11.0 nTPM
Stomach	11.0 nTPM
Thymus	9.0 nTPM
Esophagus	5.9 nTPM
Adipose tissue	5.8 nTPM
Salivary gland	5.1 nTPM
Skin	1.7 nTPM
Lung	1.3 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM

Ciliated cells	4.2 nTPM
Bronchus	5.2 nTPM
Endometrium	4.6 nTPM
Lung	4.0 nTPM
Fallopian tube	2.8 nTPM

Club cells	3.8 nTPM
Prostate	5.6 nTPM
Bronchus	3.4 nTPM
Lung	2.4 nTPM

Endothelial cells	3.5 nTPM
Heart muscle	5.2 nTPM
Pancreas	5.2 nTPM
Liver	5.0 nTPM
Prostate	4.8 nTPM
Placenta	4.5 nTPM
Esophagus	4.3 nTPM
Thymus	4.0 nTPM
Ovary	3.7 nTPM
Endometrium	3.6 nTPM
Tongue	3.6 nTPM
Skeletal muscle	3.1 nTPM
Vascular	3.1 nTPM
Testis	2.7 nTPM
Salivary gland	2.6 nTPM
Breast	2.6 nTPM
Fallopian tube	2.1 nTPM
Skin	1.7 nTPM
Lung	1.7 nTPM

Enteroendocrine cells	4.8 nTPM
Rectum	6.7 nTPM
Colon	4.3 nTPM
Small intestine	3.4 nTPM

Fibroblasts	4.4 nTPM
Stomach	8.6 nTPM
Prostate	6.6 nTPM
Liver	5.9 nTPM
Esophagus	5.8 nTPM
Thymus	4.8 nTPM
Breast	4.6 nTPM
Adipose tissue	3.9 nTPM
Skeletal muscle	3.8 nTPM
Skin	3.7 nTPM
Salivary gland	3.7 nTPM
Placenta	3.6 nTPM
Vascular	3.6 nTPM
Lung	3.5 nTPM
Fallopian tube	3.5 nTPM
Heart muscle	2.5 nTPM
Pancreas	2.2 nTPM

Granulocytes	11.5 nTPM
Tongue	19.4 nTPM
Fallopian tube	8.5 nTPM
Lung	6.6 nTPM

Intestinal goblet cells	3.7 nTPM
Rectum	5.2 nTPM
Colon	3.7 nTPM
Small intestine	2.3 nTPM

Lymphatic endothelial cells	3.5 nTPM
Ovary	5.5 nTPM
Fallopian tube	1.5 nTPM

Macrophages	4.4 nTPM
Skin	12.3 nTPM
Spleen	9.0 nTPM
Esophagus	6.4 nTPM
Salivary gland	5.6 nTPM
Stomach	5.1 nTPM
Thymus	5.1 nTPM
Adipose tissue	4.3 nTPM
Prostate	4.3 nTPM
Bone marrow	4.1 nTPM
Vascular	4.0 nTPM
Fallopian tube	4.0 nTPM
Endometrium	3.7 nTPM
Tongue	3.7 nTPM
Breast	3.7 nTPM
Lung	3.0 nTPM
Kidney	2.7 nTPM
Skeletal muscle	1.7 nTPM
Testis	1.2 nTPM
Pancreas	0.0 nTPM

Paneth cells	3.4 nTPM
Colon	3.6 nTPM
Small intestine	3.5 nTPM
Rectum	3.2 nTPM

Basal prostatic cells	4.9 nTPM
Prostate	4.9 nTPM

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Endometrial stromal cells	5.4 nTPM
Endometrium	5.4 nTPM

Plasma cells	4.0 nTPM
Stomach	13.0 nTPM
Thymus	6.4 nTPM
Spleen	4.8 nTPM
Salivary gland	2.7 nTPM
Fallopian tube	1.9 nTPM
Liver	1.5 nTPM
Bone marrow	1.5 nTPM
Esophagus	0.0 nTPM

Schwann cells	1.4 nTPM
Vascular	3.1 nTPM
Adipose tissue	1.2 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	4.6 nTPM
Salivary gland	4.8 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	5.2 nTPM
Skin	7.4 nTPM
Thymus	7.2 nTPM
Esophagus	6.0 nTPM
Vascular	5.9 nTPM
Salivary gland	5.8 nTPM
Breast	5.6 nTPM
Prostate	5.5 nTPM
Fallopian tube	5.5 nTPM
Ovary	5.1 nTPM
Endometrium	4.7 nTPM
Lung	4.7 nTPM
Tongue	4.5 nTPM
Placenta	4.2 nTPM
Adipose tissue	4.0 nTPM
Skeletal muscle	3.8 nTPM
Liver	2.5 nTPM

T-cells	18.9 nTPM
Stomach	50.1 nTPM
Thymus	29.7 nTPM
Spleen	26.4 nTPM
Bone marrow	26.2 nTPM
Lymph node	24.1 nTPM
Breast	23.5 nTPM
Endometrium	20.2 nTPM
Esophagus	17.0 nTPM
Colon	16.6 nTPM
Liver	16.5 nTPM
Salivary gland	15.6 nTPM
Skin	15.4 nTPM
Prostate	14.7 nTPM
Fallopian tube	14.6 nTPM
Adipose tissue	14.4 nTPM
PBMC	13.2 nTPM
Vascular	12.9 nTPM
Tongue	12.8 nTPM
Lung	12.7 nTPM
Skeletal muscle	11.7 nTPM
Kidney	8.0 nTPM

Undifferentiated cells	3.9 nTPM
Rectum	5.1 nTPM
Colon	3.4 nTPM
Small intestine	3.2 nTPM

Amygdala excitatory	33.8 nTPM
Hypothalamus	40.1 nTPM
Amygdala	35.1 nTPM
Thalamus	33.1 nTPM
Cerebral cortex	31.9 nTPM
Hippocampus	31.8 nTPM
Basal ganglia	31.0 nTPM

Astrocyte	33.5 nTPM
Cerebellum	43.5 nTPM
Thalamus	36.2 nTPM
Midbrain	35.6 nTPM
Spinal cord	35.6 nTPM
Pons	35.2 nTPM
Medulla oblongata	33.4 nTPM
Amygdala	31.6 nTPM
Cerebral cortex	31.3 nTPM
Hippocampus	31.0 nTPM
Basal ganglia	27.4 nTPM
Hypothalamus	27.3 nTPM

Bergmann glia	22.2 nTPM
Pons	37.4 nTPM
Cerebellum	22.8 nTPM
Medulla oblongata	6.4 nTPM

Central nervous system macrophage	22.2 nTPM
Amygdala	26.3 nTPM
Hippocampus	25.0 nTPM
Midbrain	24.9 nTPM
Cerebellum	24.4 nTPM
Cerebral cortex	22.4 nTPM
Pons	22.4 nTPM
Thalamus	21.9 nTPM
Hypothalamus	20.7 nTPM
Spinal cord	19.1 nTPM
Medulla oblongata	18.4 nTPM
Basal ganglia	18.3 nTPM

Cerebellar inhibitory	29.0 nTPM
Spinal cord	33.0 nTPM
Cerebellum	29.9 nTPM
Midbrain	29.2 nTPM
Medulla oblongata	28.5 nTPM
Pons	24.4 nTPM

Cge interneuron	33.4 nTPM
Hypothalamus	45.9 nTPM
Amygdala	34.9 nTPM
Hippocampus	34.2 nTPM
Cerebral cortex	33.1 nTPM
Basal ganglia	31.4 nTPM
Thalamus	27.4 nTPM
Midbrain	27.0 nTPM

Choroid plexus epithelial cell	32.8 nTPM
Basal ganglia	41.6 nTPM
Hippocampus	41.6 nTPM
Thalamus	24.7 nTPM
Medulla oblongata	23.5 nTPM

Committed oligodendrocyte precursor	26.3 nTPM
Amygdala	37.8 nTPM
Hypothalamus	32.8 nTPM
Pons	32.8 nTPM
Thalamus	32.0 nTPM
Cerebral cortex	29.1 nTPM
Cerebellum	27.0 nTPM
Midbrain	26.9 nTPM
Hippocampus	24.8 nTPM
Basal ganglia	20.3 nTPM
Medulla oblongata	18.1 nTPM
Spinal cord	7.4 nTPM

Deep-layer corticothalamic and 6b	33.7 nTPM
Hypothalamus	46.0 nTPM
Basal ganglia	34.2 nTPM
Amygdala	33.7 nTPM
Hippocampus	33.4 nTPM
Cerebral cortex	32.5 nTPM
Midbrain	22.2 nTPM

Deep-layer intratelencephalic	33.5 nTPM
Hypothalamus	46.9 nTPM
Amygdala	31.9 nTPM
Cerebral cortex	30.1 nTPM
Basal ganglia	29.9 nTPM
Hippocampus	28.5 nTPM

Deep-layer near-projecting	37.0 nTPM
Hypothalamus	57.6 nTPM
Cerebral cortex	36.3 nTPM
Amygdala	34.6 nTPM
Basal ganglia	30.5 nTPM
Hippocampus	26.0 nTPM

Eccentric medium spiny neuron	30.8 nTPM
Hypothalamus	35.0 nTPM
Hippocampus	31.5 nTPM
Basal ganglia	30.3 nTPM
Amygdala	29.4 nTPM
Cerebral cortex	29.4 nTPM
Thalamus	29.3 nTPM

Endothelial cell	18.6 nTPM
Amygdala	25.7 nTPM
Midbrain	21.7 nTPM
Basal ganglia	21.4 nTPM
Spinal cord	20.7 nTPM
Cerebral cortex	19.2 nTPM
Hippocampus	19.2 nTPM
Hypothalamus	17.4 nTPM
Thalamus	16.4 nTPM
Pons	15.6 nTPM
Medulla oblongata	14.4 nTPM
Cerebellum	12.4 nTPM

Ependymal cell	22.7 nTPM
Amygdala	29.6 nTPM
Basal ganglia	24.1 nTPM
Hippocampus	23.6 nTPM
Hypothalamus	23.2 nTPM
Spinal cord	23.0 nTPM
Midbrain	22.2 nTPM
Thalamus	20.7 nTPM
Medulla oblongata	19.8 nTPM
Pons	18.5 nTPM