Single cell type - USP11 - The Human Protein Atlas

USP11

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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.	USP11
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 11
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Metabolic proteins Plasma 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.	4

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.	Bipolar cells - Visual perception (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 enhanced (Bipolar cells, Horizontal cells)
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.	0.36
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: Cell type enhanced (Bipolar cells, Horizontal cells)

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

USP11 is part of cluster 25 Bipolar cells - Visual perception with confidenceⁱ 1
152 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.
ATP6V1G2	ATPase H+ transporting V1 subunit G2	0.6959	25
GABRR1	Gamma-aminobutyric acid type A receptor subunit rho1	0.6820	25
TCEAL6	Transcription elongation factor A like 6	0.6787	25
MC4R	Melanocortin 4 receptor	0.6720	25
SYNDIG1L	Synapse differentiation inducing 1 like	0.6624	25
GPR179	G protein-coupled receptor 179	0.6595	25
LRTM1	Leucine rich repeats and transmembrane domains 1	0.6571	25
TRPM1	Transient receptor potential cation channel subfamily M member 1	0.6536	25
VSX2	Visual system homeobox 2	0.6536	25
GNG13	G protein subunit gamma 13	0.6517	25
TAB1	TGF-beta activated kinase 1 (MAP3K7) binding protein 1	0.6513	25
GRM6	Glutamate metabotropic receptor 6	0.6496	25
AANAT	Aralkylamine N-acetyltransferase	0.6459	25
CRHR1	Corticotropin releasing hormone receptor 1	0.6449	25
ENSG00000269533	Novel transcript	0.6434	25

IMMUNE CELLS

USP11 is part of cluster 5 Non-specific - Cell proliferation with confidenceⁱ 1
689 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.
MSANTD7	Myb/SANT DNA binding domain containing 7	1.0000	5
CENPP	Centromere protein P	1.0000	5
HSPA13	Heat shock protein family A (Hsp70) member 13	1.0000	5
ZNF490	Zinc finger protein 490	0.9762	32
NCOA7	Nuclear receptor coactivator 7	0.9762	41
OGG1	8-oxoguanine DNA glycosylase	0.9762	5
MRE11	MRE11 homolog, double strand break repair nuclease	0.9762	5
MCEE	Methylmalonyl-CoA epimerase	0.9762	5
CCDC91	Coiled-coil domain containing 91	0.9524	32
PGAM5	PGAM family member 5, mitochondrial serine/threonine protein phosphatase	0.9524	5
ANKRD40	Ankyrin repeat domain 40	0.9524	5
COG3	Component of oligomeric golgi complex 3	0.9524	41
RAB2B	RAB2B, member RAS oncogene family	0.9524	5
TARS1	Threonyl-tRNA synthetase 1	0.9286	5
BEX4	Brain expressed X-linked 4	0.9286	41

Adipocytes	13.4 nTPM
Breast	14.1 nTPM
Adipose tissue	12.7 nTPM

Alveolar cells type 1	22.2 nTPM
Lung	22.2 nTPM

Alveolar cells type 2	26.7 nTPM
Lung	26.7 nTPM

Astrocytes	24.5 nTPM
Brain	24.5 nTPM

B-cells	45.9 nTPM
Stomach	102.1 nTPM
Lymph node	81.1 nTPM
Spleen	69.4 nTPM
Thymus	62.2 nTPM
Salivary gland	43.4 nTPM
Adipose tissue	42.8 nTPM
Esophagus	41.3 nTPM
Bone marrow	39.4 nTPM
Lung	34.9 nTPM
Skin	28.8 nTPM
PBMC	21.6 nTPM
Kidney	20.8 nTPM
Liver	9.7 nTPM

Ciliated cells	42.5 nTPM
Lung	50.2 nTPM
Fallopian tube	49.8 nTPM
Bronchus	40.4 nTPM
Endometrium	29.5 nTPM

Club cells	26.4 nTPM
Bronchus	32.5 nTPM
Lung	25.9 nTPM
Prostate	20.8 nTPM

Dendritic cells	78.0 nTPM
Adipose tissue	112.8 nTPM
PBMC	43.2 nTPM

Endothelial cells	18.7 nTPM
Liver	31.5 nTPM
Ovary	28.8 nTPM
Placenta	26.7 nTPM
Fallopian tube	24.8 nTPM
Pancreas	23.3 nTPM
Prostate	22.6 nTPM
Breast	22.0 nTPM
Lung	19.9 nTPM
Esophagus	17.7 nTPM
Endometrium	16.8 nTPM
Salivary gland	16.6 nTPM
Thymus	16.1 nTPM
Heart muscle	14.5 nTPM
Skeletal muscle	13.6 nTPM
Testis	11.0 nTPM
Vascular	11.0 nTPM
Tongue	10.5 nTPM
Skin	10.2 nTPM

Enteroendocrine cells	23.5 nTPM
Rectum	38.6 nTPM
Small intestine	24.0 nTPM
Colon	7.8 nTPM

Fibroblasts	38.1 nTPM
Fallopian tube	67.4 nTPM
Placenta	58.5 nTPM
Stomach	57.6 nTPM
Esophagus	50.6 nTPM
Prostate	44.2 nTPM
Skeletal muscle	39.8 nTPM
Lung	35.0 nTPM
Thymus	34.6 nTPM
Breast	33.0 nTPM
Skin	32.4 nTPM
Adipose tissue	31.3 nTPM
Pancreas	28.9 nTPM
Vascular	27.6 nTPM
Salivary gland	26.6 nTPM
Liver	23.7 nTPM
Heart muscle	18.2 nTPM

Granulocytes	65.0 nTPM
Fallopian tube	71.3 nTPM
Lung	65.5 nTPM
Tongue	58.2 nTPM

Intestinal goblet cells	8.7 nTPM
Colon	10.1 nTPM
Rectum	8.6 nTPM
Small intestine	7.4 nTPM

Lymphatic endothelial cells	17.9 nTPM
Fallopian tube	30.4 nTPM
Ovary	5.5 nTPM

Macrophages	18.2 nTPM
Lung	37.3 nTPM
Adipose tissue	25.8 nTPM
Fallopian tube	24.5 nTPM
Esophagus	24.4 nTPM
Stomach	23.1 nTPM
Salivary gland	23.1 nTPM
Pancreas	20.6 nTPM
Prostate	20.3 nTPM
Spleen	20.1 nTPM
Breast	19.6 nTPM
Skin	17.8 nTPM
Thymus	15.2 nTPM
Skeletal muscle	12.7 nTPM
Endometrium	12.3 nTPM
Kidney	10.6 nTPM
Tongue	10.3 nTPM
Vascular	10.3 nTPM
Testis	9.9 nTPM
Bone marrow	7.1 nTPM

Basal keratinocytes	11.7 nTPM
Skin	14.0 nTPM
Tongue	9.4 nTPM

Basal prostatic cells	39.6 nTPM
Prostate	39.6 nTPM

Basal respiratory cells	30.5 nTPM
Bronchus	30.5 nTPM

Basal squamous epithelial cells	16.2 nTPM
Esophagus	16.2 nTPM

Paneth cells	6.7 nTPM
Rectum	9.5 nTPM
Small intestine	6.9 nTPM
Colon	3.6 nTPM

Plasma cells	39.9 nTPM
Stomach	82.9 nTPM
Fallopian tube	49.2 nTPM
Spleen	42.8 nTPM
Thymus	37.6 nTPM
Esophagus	36.4 nTPM
Bone marrow	25.7 nTPM
Salivary gland	24.6 nTPM
Liver	20.0 nTPM

Schwann cells	39.2 nTPM
Vascular	66.9 nTPM
Esophagus	35.9 nTPM
Adipose tissue	14.8 nTPM

Serous glandular cells	12.9 nTPM
Salivary gland	17.0 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	41.0 nTPM
Fallopian tube	71.3 nTPM
Lung	64.7 nTPM
Esophagus	57.7 nTPM
Ovary	45.7 nTPM
Thymus	44.4 nTPM
Placenta	44.0 nTPM
Prostate	42.6 nTPM
Skeletal muscle	38.1 nTPM
Skin	37.0 nTPM
Adipose tissue	35.6 nTPM
Vascular	33.5 nTPM
Breast	33.3 nTPM
Salivary gland	32.3 nTPM
Tongue	30.2 nTPM
Endometrium	27.5 nTPM
Liver	18.3 nTPM

T-cells	41.5 nTPM
Stomach	104.8 nTPM
Colon	68.2 nTPM
Spleen	67.6 nTPM
Lymph node	60.4 nTPM
Bone marrow	49.5 nTPM
Thymus	49.1 nTPM
Adipose tissue	43.5 nTPM
Fallopian tube	41.9 nTPM
Prostate	38.8 nTPM
Salivary gland	36.6 nTPM
Breast	33.2 nTPM
Lung	32.4 nTPM
Kidney	31.9 nTPM
Liver	30.6 nTPM
Skeletal muscle	30.2 nTPM
Vascular	27.3 nTPM
Endometrium	26.9 nTPM
Esophagus	26.8 nTPM
PBMC	26.0 nTPM
Tongue	23.5 nTPM
Skin	22.8 nTPM

Undifferentiated cells	9.8 nTPM
Colon	11.0 nTPM
Rectum	10.3 nTPM
Small intestine	8.1 nTPM

Amygdala excitatory	76.2 nTPM
Thalamus	98.5 nTPM
Hypothalamus	81.2 nTPM
Basal ganglia	79.8 nTPM
Hippocampus	68.2 nTPM
Amygdala	66.8 nTPM
Cerebral cortex	62.6 nTPM

Astrocyte	44.9 nTPM
Spinal cord	54.3 nTPM
Cerebellum	52.0 nTPM
Thalamus	48.7 nTPM
Cerebral cortex	48.3 nTPM
Midbrain	45.3 nTPM
Pons	45.2 nTPM
Hypothalamus	42.8 nTPM
Medulla oblongata	42.5 nTPM
Hippocampus	38.9 nTPM
Amygdala	38.6 nTPM
Basal ganglia	37.5 nTPM

Bergmann glia	28.8 nTPM
Cerebellum	34.2 nTPM
Medulla oblongata	32.0 nTPM
Pons	20.1 nTPM

Central nervous system macrophage	30.3 nTPM
Cerebral cortex	38.0 nTPM
Thalamus	36.9 nTPM
Hypothalamus	33.7 nTPM
Hippocampus	31.1 nTPM
Spinal cord	30.9 nTPM
Amygdala	29.6 nTPM
Midbrain	28.6 nTPM
Basal ganglia	27.8 nTPM
Pons	27.0 nTPM
Cerebellum	26.3 nTPM
Medulla oblongata	23.8 nTPM

Cerebellar inhibitory	81.1 nTPM
Spinal cord	104.5 nTPM
Cerebellum	80.8 nTPM
Midbrain	80.6 nTPM
Pons	80.0 nTPM
Medulla oblongata	59.7 nTPM

Cge interneuron	158.7 nTPM
Thalamus	176.6 nTPM
Cerebral cortex	166.2 nTPM
Hypothalamus	159.6 nTPM
Midbrain	158.2 nTPM
Basal ganglia	152.9 nTPM
Hippocampus	152.1 nTPM
Amygdala	145.3 nTPM

Choroid plexus epithelial cell	32.2 nTPM
Hippocampus	38.8 nTPM
Medulla oblongata	35.3 nTPM
Basal ganglia	32.5 nTPM
Thalamus	21.9 nTPM

Committed oligodendrocyte precursor	54.2 nTPM
Cerebral cortex	70.9 nTPM
Spinal cord	62.5 nTPM
Midbrain	58.8 nTPM
Hypothalamus	58.7 nTPM
Hippocampus	54.3 nTPM
Medulla oblongata	52.9 nTPM
Pons	51.3 nTPM
Thalamus	50.9 nTPM
Basal ganglia	49.3 nTPM
Cerebellum	46.0 nTPM
Amygdala	40.6 nTPM

Deep-layer corticothalamic and 6b	80.7 nTPM
Hypothalamus	96.7 nTPM
Midbrain	88.8 nTPM
Basal ganglia	83.8 nTPM
Amygdala	77.1 nTPM
Cerebral cortex	75.4 nTPM
Hippocampus	62.7 nTPM

Deep-layer intratelencephalic	79.8 nTPM
Hypothalamus	112.2 nTPM
Cerebral cortex	82.6 nTPM
Amygdala	71.2 nTPM
Basal ganglia	70.8 nTPM
Hippocampus	62.2 nTPM

Deep-layer near-projecting	93.7 nTPM
Hypothalamus	126.1 nTPM
Cerebral cortex	93.7 nTPM
Amygdala	88.9 nTPM
Basal ganglia	83.1 nTPM
Hippocampus	76.8 nTPM

Eccentric medium spiny neuron	137.9 nTPM
Hypothalamus	179.3 nTPM
Thalamus	150.5 nTPM
Hippocampus	140.9 nTPM
Cerebral cortex	120.8 nTPM
Basal ganglia	118.4 nTPM
Amygdala	117.3 nTPM

Endothelial cell	24.8 nTPM
Cerebral cortex	36.4 nTPM
Hypothalamus	28.5 nTPM
Hippocampus	27.6 nTPM
Thalamus	26.0 nTPM
Cerebellum	25.6 nTPM
Amygdala	23.5 nTPM
Basal ganglia	23.3 nTPM
Spinal cord	22.4 nTPM
Midbrain	21.7 nTPM
Medulla oblongata	19.5 nTPM
Pons	18.1 nTPM