Single cell type - USP54 - The Human Protein Atlas

USP54

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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.	USP54
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 54
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	15

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.	Oligodendrocytes - Unknown function (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.	Cell type enriched (Oligodendrocytes)
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.	0.65
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.	Cell type enhanced (Oligodendrocyte, Endothelial cell)
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.	Not detected in immune cells
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: Cell type enriched (Oligodendrocytes)

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: Cell type enhanced (Oligodendrocyte, Endothelial cell)

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: Not detected in immune cells
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

USP54 is part of cluster 51 Oligodendrocytes - Unknown function with confidenceⁱ 1
302 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.
HHIP	Hedgehog interacting protein	0.7241	72
PLEKHH1	Pleckstrin homology, MyTH4 and FERM domain containing H1	0.6509	51
PRUNE2	Prune homolog 2 with BCH domain	0.6357	51
UGT8	UDP glycosyltransferase 8	0.6308	51
NMUR2	Neuromedin U receptor 2	0.6159	51
NCKAP5	NCK associated protein 5	0.6153	51
SHROOM4	Shroom family member 4	0.6151	51
SLCO1A2	Solute carrier organic anion transporter family member 1A2	0.6083	51
CARNS1	Carnosine synthase 1	0.6056	51
SLC5A11	Solute carrier family 5 member 11	0.6026	51
LGI3	Leucine rich repeat LGI family member 3	0.5984	72
RNF220	Ring finger protein 220	0.5972	51
TMEM235	Transmembrane protein 235	0.5957	51
SLAIN1	SLAIN motif family member 1	0.5940	51
PHLPP1	PH domain and leucine rich repeat protein phosphatase 1	0.5938	51

IMMUNE CELLS

USP54 is part of cluster 16 Non-specific - Cell proliferation with confidenceⁱ 1
161 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.
SHMT1	Serine hydroxymethyltransferase 1	1.0000	16
DTL	Denticleless E3 ubiquitin protein ligase homolog	0.9762	16
RGPD2	RANBP2 like and GRIP domain containing 2	0.9762	16
AURKB	Aurora kinase B	0.9762	16
GPR25	G protein-coupled receptor 25	0.9762	16
MS4A15	Membrane spanning 4-domains A15	0.9762	16
PCLAF	PCNA clamp associated factor	0.9762	16
TSHR	Thyroid stimulating hormone receptor	0.9762	16
EYA3	EYA transcriptional coactivator and phosphatase 3	0.9762	16
CCNB2	Cyclin B2	0.9762	16
TPX2	TPX2 microtubule nucleation factor	0.9762	16
DSCC1	DNA replication and sister chromatid cohesion 1	0.9762	16
ZSWIM3	Zinc finger SWIM-type containing 3	0.9762	16
TNFRSF19	TNF receptor superfamily member 19	0.9762	16
PKMYT1	Protein kinase, membrane associated tyrosine/threonine 1	0.9762	16

Adipocytes	5.7 nTPM
Adipose tissue	7.7 nTPM
Breast	3.7 nTPM

Alveolar cells type 1	35.6 nTPM
Lung	35.6 nTPM

Alveolar cells type 2	66.2 nTPM
Lung	66.2 nTPM

Astrocytes	31.3 nTPM
Brain	31.3 nTPM

B-cells	2.8 nTPM
Skin	6.8 nTPM
Esophagus	5.9 nTPM
Lung	4.0 nTPM
Thymus	3.9 nTPM
Stomach	3.8 nTPM
Salivary gland	2.8 nTPM
Lymph node	2.6 nTPM
Adipose tissue	2.5 nTPM
Bone marrow	1.6 nTPM
PBMC	1.5 nTPM
Spleen	0.7 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM

Ciliated cells	25.7 nTPM
Lung	33.5 nTPM
Bronchus	29.6 nTPM
Endometrium	23.3 nTPM
Fallopian tube	16.3 nTPM

Club cells	31.2 nTPM
Prostate	40.7 nTPM
Lung	32.2 nTPM
Bronchus	20.7 nTPM

Endothelial cells	7.1 nTPM
Thymus	11.7 nTPM
Prostate	11.4 nTPM
Salivary gland	11.3 nTPM
Vascular	11.2 nTPM
Skeletal muscle	10.5 nTPM
Esophagus	9.5 nTPM
Lung	9.3 nTPM
Fallopian tube	8.7 nTPM
Ovary	8.7 nTPM
Tongue	7.6 nTPM
Testis	7.3 nTPM
Heart muscle	6.1 nTPM
Endometrium	5.9 nTPM
Skin	5.0 nTPM
Breast	1.8 nTPM
Liver	1.3 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	12.5 nTPM
Rectum	16.8 nTPM
Colon	13.9 nTPM
Small intestine	6.9 nTPM

Fibroblasts	7.7 nTPM
Heart muscle	17.7 nTPM
Vascular	14.6 nTPM
Esophagus	11.9 nTPM
Thymus	11.4 nTPM
Prostate	11.2 nTPM
Skeletal muscle	9.7 nTPM
Salivary gland	9.1 nTPM
Fallopian tube	8.7 nTPM
Lung	8.5 nTPM
Adipose tissue	6.0 nTPM
Stomach	4.3 nTPM
Skin	3.2 nTPM
Breast	2.0 nTPM
Placenta	1.9 nTPM
Pancreas	1.6 nTPM
Liver	1.2 nTPM

Granulocytes	2.7 nTPM
Lung	4.5 nTPM
Fallopian tube	3.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	27.6 nTPM
Small intestine	36.7 nTPM
Rectum	24.8 nTPM
Colon	21.4 nTPM

Lymphatic endothelial cells	2.1 nTPM
Fallopian tube	4.1 nTPM
Ovary	0.0 nTPM

Macrophages	1.5 nTPM
Vascular	4.1 nTPM
Salivary gland	3.8 nTPM
Endometrium	3.7 nTPM
Fallopian tube	2.5 nTPM
Lung	2.4 nTPM
Prostate	2.1 nTPM
Adipose tissue	1.7 nTPM
Tongue	1.7 nTPM
Esophagus	1.3 nTPM
Testis	1.2 nTPM
Thymus	1.2 nTPM
Breast	1.2 nTPM
Skin	1.1 nTPM
Bone marrow	1.0 nTPM
Skeletal muscle	0.4 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	9.4 nTPM
Rectum	17.7 nTPM
Small intestine	6.9 nTPM
Colon	3.6 nTPM

Basal respiratory cells	10.8 nTPM
Bronchus	10.8 nTPM

Basal squamous epithelial cells	5.1 nTPM
Esophagus	5.1 nTPM

Bipolar cells	6.5 nTPM
Eye	6.5 nTPM

Collecting duct cells	13.6 nTPM
Kidney	13.6 nTPM

Plasma cells	3.0 nTPM
Salivary gland	6.7 nTPM
Esophagus	5.2 nTPM
Fallopian tube	3.5 nTPM
Thymus	2.6 nTPM
Spleen	1.9 nTPM
Bone marrow	1.5 nTPM
Stomach	1.3 nTPM
Liver	1.0 nTPM

Schwann cells	13.4 nTPM
Esophagus	24.0 nTPM
Vascular	15.1 nTPM
Adipose tissue	1.2 nTPM

Serous glandular cells	11.0 nTPM
Salivary gland	17.7 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	4.9 nTPM
Salivary gland	15.2 nTPM
Tongue	12.6 nTPM
Vascular	8.2 nTPM
Fallopian tube	7.2 nTPM
Thymus	6.0 nTPM
Endometrium	5.9 nTPM
Skeletal muscle	4.0 nTPM
Skin	3.6 nTPM
Prostate	3.6 nTPM
Ovary	2.7 nTPM
Adipose tissue	2.4 nTPM
Lung	2.4 nTPM
Breast	1.8 nTPM
Placenta	1.3 nTPM
Liver	0.8 nTPM
Esophagus	0.0 nTPM

Suprabasal keratinocytes	11.5 nTPM
Tongue	19.0 nTPM
Skin	4.0 nTPM

T-cells	2.6 nTPM
Esophagus	7.3 nTPM
Salivary gland	4.4 nTPM
Endometrium	4.0 nTPM
Vascular	4.0 nTPM
Skin	3.5 nTPM
Tongue	3.4 nTPM
Lymph node	3.0 nTPM
Thymus	2.7 nTPM
Skeletal muscle	2.6 nTPM
Stomach	2.2 nTPM
Lung	2.1 nTPM
Prostate	2.0 nTPM
Adipose tissue	1.9 nTPM
Kidney	1.8 nTPM
Breast	1.7 nTPM
Fallopian tube	1.7 nTPM
PBMC	1.5 nTPM
Bone marrow	1.5 nTPM
Colon	1.0 nTPM
Spleen	0.9 nTPM
Liver	0.7 nTPM

Undifferentiated cells	8.6 nTPM
Rectum	11.3 nTPM
Colon	7.4 nTPM
Small intestine	7.0 nTPM

Amygdala excitatory	63.1 nTPM
Thalamus	118.4 nTPM
Hypothalamus	67.1 nTPM
Basal ganglia	62.7 nTPM
Amygdala	44.1 nTPM
Cerebral cortex	43.4 nTPM
Hippocampus	42.8 nTPM

Astrocyte	210.3 nTPM
Spinal cord	507.9 nTPM
Medulla oblongata	288.3 nTPM
Hypothalamus	223.3 nTPM
Pons	204.1 nTPM
Cerebellum	195.1 nTPM
Amygdala	172.5 nTPM
Midbrain	170.4 nTPM
Basal ganglia	154.8 nTPM
Hippocampus	135.2 nTPM
Thalamus	131.3 nTPM
Cerebral cortex	130.8 nTPM

Bergmann glia	119.6 nTPM
Cerebellum	126.6 nTPM
Medulla oblongata	117.2 nTPM
Pons	115.1 nTPM

Central nervous system macrophage	34.0 nTPM
Spinal cord	43.0 nTPM
Amygdala	39.2 nTPM
Midbrain	37.4 nTPM
Hypothalamus	35.2 nTPM
Hippocampus	34.5 nTPM
Cerebral cortex	34.4 nTPM
Basal ganglia	33.0 nTPM
Cerebellum	32.6 nTPM
Pons	30.7 nTPM
Thalamus	29.5 nTPM
Medulla oblongata	24.6 nTPM

Cerebellar inhibitory	89.2 nTPM
Spinal cord	107.2 nTPM
Cerebellum	92.9 nTPM
Medulla oblongata	90.8 nTPM
Midbrain	87.7 nTPM
Pons	67.6 nTPM

Cge interneuron	71.6 nTPM
Hypothalamus	98.7 nTPM
Amygdala	83.2 nTPM
Basal ganglia	71.3 nTPM
Cerebral cortex	70.6 nTPM
Hippocampus	65.1 nTPM
Thalamus	56.4 nTPM
Midbrain	56.0 nTPM

Choroid plexus epithelial cell	183.8 nTPM
Basal ganglia	225.6 nTPM
Thalamus	211.0 nTPM
Medulla oblongata	162.8 nTPM
Hippocampus	135.9 nTPM

Committed oligodendrocyte precursor	461.3 nTPM
Amygdala	682.8 nTPM
Cerebral cortex	656.1 nTPM
Hypothalamus	612.5 nTPM
Thalamus	604.9 nTPM
Hippocampus	589.8 nTPM
Basal ganglia	415.0 nTPM
Midbrain	379.7 nTPM
Cerebellum	350.4 nTPM
Spinal cord	316.4 nTPM
Pons	248.8 nTPM
Medulla oblongata	218.2 nTPM

Deep-layer corticothalamic and 6b	61.2 nTPM
Hypothalamus	75.8 nTPM
Hippocampus	69.1 nTPM
Amygdala	65.7 nTPM
Midbrain	62.1 nTPM
Cerebral cortex	48.0 nTPM
Basal ganglia	46.4 nTPM

Deep-layer intratelencephalic	44.4 nTPM
Hypothalamus	57.3 nTPM
Cerebral cortex	44.9 nTPM
Amygdala	43.0 nTPM
Basal ganglia	39.8 nTPM
Hippocampus	36.8 nTPM

Deep-layer near-projecting	111.1 nTPM
Hypothalamus	127.4 nTPM
Amygdala	126.5 nTPM
Basal ganglia	109.0 nTPM
Cerebral cortex	98.1 nTPM
Hippocampus	94.6 nTPM

Eccentric medium spiny neuron	62.5 nTPM
Hippocampus	82.1 nTPM
Hypothalamus	67.4 nTPM
Amygdala	66.1 nTPM
Cerebral cortex	61.0 nTPM
Thalamus	52.2 nTPM
Basal ganglia	46.1 nTPM

Endothelial cell	823.7 nTPM
Hypothalamus	1337.4 nTPM
Spinal cord	1023.5 nTPM
Medulla oblongata	849.2 nTPM
Midbrain	847.7 nTPM
Cerebellum	843.3 nTPM
Cerebral cortex	815.1 nTPM
Amygdala	759.0 nTPM
Hippocampus	700.4 nTPM
Thalamus	672.1 nTPM
Pons	671.6 nTPM
Basal ganglia	541.5 nTPM